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. 2005 Dec 2;33(21):6823–6836. doi: 10.1093/nar/gki987

Figure 1.

Figure 1

An Alu consensus DNA sequence determined from the sequences of young and old individual Alu repeats. Old Alu sequences (Alu-J, SluSp, AluSx, AluSq and AluSc) and young Alu sequences (AluY, AluSb2, AluYb8, AluYa5 and AluYa8) were compared in order to generate an Alu consensus sequence for the purpose of designing an Alu-based MethyLight control reaction. Since the goal was to design a methylation-independent reaction of as many individual Alu repeats as possible, all CpG dinucleotides became a part of the consensus sequence. Old Alu sequences are the predominant form in human cells, and this is also reflected in the Alu consensus sequence. The continuous and dashed lines underneath the consensus sequence panels indicate the MethyLight PCR amplicon locations within the consensus sequence for the Alu control reaction (ALU-C4), two reactions toward the methylated consensus sequence (ALU-M2 and ALU-M3) and one reaction toward the unmethylated Alu consensus sequence (ALU-U3).